Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 5 of 100
Found at i:931505 original size:7 final size:7
Alignment explanation
Indices: 931356--931524 Score: 69
Period size: 7 Copynumber: 23.4 Consensus size: 7
931346 AGGTTTTTTA
*
931356 TTTAGGG
1 TTTAAGG
931363 TTT-AGG
1 TTTAAGG
931369 TTTAAGG
1 TTTAAGG
931376 TTTAAGG
1 TTTAAGG
* *
931383 TTTTAGT
1 TTTAAGG
*
931390 TTTACGG
1 TTTAAGG
*
931397 TTTGGAGG
1 TTT-AAGG
*
931405 ATTTAGGG
1 -TTTAAGG
*
931413 TTTTAA-T
1 -TTTAAGG
931420 TTTAAGG
1 TTTAAGG
931427 TTTAAGGGG
1 TTTAA--GG
*
931436 TTTAGGG
1 TTTAAGG
*
931443 TTTAA-T
1 TTTAAGG
931449 TTTAAGG
1 TTTAAGG
*
931456 TTTGGAGG
1 TTT-AAGG
*
931464 TTTAGGGG
1 TTTA-AGG
* *
931472 TTTGA-T
1 TTTAAGG
*
931478 TTTAGGG
1 TTTAAGG
931485 TTTTAAGGG
1 -TTTAA-GG
931494 TTTAAGG
1 TTTAAGG
*
931501 TTTAA-T
1 TTTAAGG
*
931507 TTTAGGG
1 TTTAAGG
931514 TTTGAAGG
1 TTT-AAGG
931522 TTT
1 TTT
931525 GGGATTTTGA
Statistics
Matches: 116, Mismatches: 32, Indels: 27
0.66 0.18 0.15
Matches are distributed among these distances:
6 22 0.19
7 49 0.42
8 34 0.29
9 11 0.09
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.47
Consensus pattern (7 bp):
TTTAAGG
Found at i:931537 original size:29 final size:30
Alignment explanation
Indices: 931363--931575 Score: 185
Period size: 29 Copynumber: 7.3 Consensus size: 30
931353 TTATTTAGGG
*
931363 TTTA-GGTTT-AA-GGTTTAAGGTTTT-AGT
1 TTTAGGGTTTGAAGGGTTTAGGGTTTTGA-T
* * * *
931390 TTTACGGTTTGGAGGATTTAGGGTTTTAAT
1 TTTAGGGTTTGAAGGGTTTAGGGTTTTGAT
* *
931420 TTTAAGGTTT-AAGGGGTTTAGGG-TTTAAT
1 TTTAGGGTTTGAA-GGGTTTAGGGTTTTGAT
* * *
931449 TTTAAGGTTTGGA-GGTTTAGGGGTTTGAT
1 TTTAGGGTTTGAAGGGTTTAGGGTTTTGAT
* * *
931478 TTTAGGGTTTTAAGGGTTTAAGG-TTTAAT
1 TTTAGGGTTTGAAGGGTTTAGGGTTTTGAT
931507 TTTAGGGTTTGAA-GGTTT-GGGATTTTGAT
1 TTTAGGGTTTGAAGGGTTTAGGG-TTTTGAT
* **
931536 TTCAGGGTTTGAAGGGTTTAGACTTTTGAT
1 TTTAGGGTTTGAAGGGTTTAGGGTTTTGAT
931566 TTTAGGGTTT
1 TTTAGGGTTT
931576 TGAAATTTAG
Statistics
Matches: 154, Mismatches: 20, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
27 6 0.04
28 19 0.12
29 67 0.44
30 60 0.39
31 2 0.01
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.47
Consensus pattern (30 bp):
TTTAGGGTTTGAAGGGTTTAGGGTTTTGAT
Found at i:931586 original size:15 final size:16
Alignment explanation
Indices: 931566--931622 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
931556 GACTTTTGAT
*
931566 TTTAGGGTTTTGAAA-
1 TTTAGGGTTTGGAAAG
931581 TTTAGGGTTTGGAAAG
1 TTTAGGGTTTGGAAAG
*
931597 TTTAGGGTTTGGAAAT
1 TTTAGGGTTTGGAAAG
931613 TTTAGGGTTT
1 TTTAGGGTTT
931623 AAAGGGTATG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 14 0.36
16 25 0.64
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.46
Consensus pattern (16 bp):
TTTAGGGTTTGGAAAG
Found at i:931638 original size:135 final size:131
Alignment explanation
Indices: 931436--931714 Score: 300
Period size: 135 Copynumber: 2.1 Consensus size: 131
931426 GTTTAAGGGG
* * * *
931436 TTTAGGGTTT-AATTTTAAGGTTTGGAGGTTTAGGGGTTTGATTTTAGGGTTTTAAGGGTTTAAG
1 TTTAGGGTTTGAAATTTAAGGTTTGGAAGTTTAGGGGTTTGATTTTAGGGTTTAAAGGGTATAAG
* *
931500 GTTTAATTTTAGGGTTT-GA-AGGTTT-GGGATTTTGATTTCAGGGTTT-GAAGGGTTTAGACTT
66 GTTTAATTTTAGGGTTTAGAGA-GTTTAGGG-TTTAG-TTTCAGGGTTTAG-AGGATTTAGACTT
*
931561 TTGAT
127 TCGAT
*
931566 TTTAGGGTTTTGAAATTTAGGGTTTGGAAAGTTTA-GGGTTTGGAAATTTTAGGGTTTAAAGGGT
1 TTTAGGG-TTTGAAATTTAAGGTTTGG-AAGTTTAGGGGTTT-G--ATTTTAGGGTTTAAAGGGT
** * * * **
931630 ATGGGGTTTGATTTTATGGTTTAGAGAGTTTAGGGTTTAGTTTTAGGGTTTAGAGGATTTAGGGT
61 ATAAGGTTTAATTTTAGGGTTTAGAGAGTTTAGGGTTTAGTTTCAGGGTTTAGAGGATTTAGACT
931695 TTCGAT
126 TTCGAT
931701 TTTAGGGTTTGAAA
1 TTTAGGGTTTGAAA
931715 GGCTTGAGGT
Statistics
Matches: 124, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
130 7 0.06
131 3 0.02
132 19 0.15
133 7 0.06
134 7 0.06
135 66 0.53
136 11 0.09
137 4 0.03
ACGTcount: A:0.22, C:0.01, G:0.32, T:0.45
Consensus pattern (131 bp):
TTTAGGGTTTGAAATTTAAGGTTTGGAAGTTTAGGGGTTTGATTTTAGGGTTTAAAGGGTATAAG
GTTTAATTTTAGGGTTTAGAGAGTTTAGGGTTTAGTTTCAGGGTTTAGAGGATTTAGACTTTCGA
T
Found at i:931642 original size:106 final size:106
Alignment explanation
Indices: 931504--931696 Score: 239
Period size: 106 Copynumber: 1.8 Consensus size: 106
931494 TTTAAGGTTT
* * * * *
931504 AATTTTAGGGTTTGAAGGTTTGGGATTTTGATTTCAGGGTTT-GAAGGGTTTAGACTTTTGATTT
1 AATTTTAGGGTTTAAAGGTATGGGAGTTTGATTTCAGGGTTTAG-AGAGTTTAGACTTTAG-TTT
*
931568 TAGGGTTTTGA-AATTTAGGGTTTGGAAAGTTTAGGGTTTGGA
64 TAGGGTTTAGAGAATTTAGGGTTTGGAAAGTTTAGGGTTTGGA
* * **
931610 AATTTTAGGGTTTAAAGGGTATGGG-GTTTGATTTTATGGTTTAGAGAGTTTAGGGTTTAGTTTT
1 AATTTTAGGGTTTAAA-GGTATGGGAGTTTGATTTCAGGGTTTAGAGAGTTTAGACTTTAGTTTT
*
931674 AGGGTTTAGAGGATTTAGGGTTT
65 AGGGTTTAGAGAATTTAGGGTTT
931697 CGATTTTAGG
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
105 13 0.18
106 52 0.71
107 8 0.11
ACGTcount: A:0.22, C:0.01, G:0.33, T:0.45
Consensus pattern (106 bp):
AATTTTAGGGTTTAAAGGTATGGGAGTTTGATTTCAGGGTTTAGAGAGTTTAGACTTTAGTTTTA
GGGTTTAGAGAATTTAGGGTTTGGAAAGTTTAGGGTTTGGA
Found at i:931665 original size:29 final size:29
Alignment explanation
Indices: 931566--931710 Score: 132
Period size: 29 Copynumber: 4.8 Consensus size: 29
931556 GACTTTTGAT
* * *
931566 TTTAGGGTTTTGAAATTTAGGGTTTGGAAAG
1 TTTAGGG-TTTG-ATTTTAGGGTTTAGAGAG
* *
931597 TTTAGGGTTTGGAAATTTTAGGGTTTAAAGGG
1 TTTAGGGTTT-G--ATTTTAGGGTTTAGAGAG
* * *
931629 TATGGGGTTTGATTTTATGGTTTAGAGAG
1 TTTAGGGTTTGATTTTAGGGTTTAGAGAG
931658 TTTAGGGTTT-AGTTTTAGGGTTTAGAG-G
1 TTTAGGGTTTGA-TTTTAGGGTTTAGAGAG
931686 ATTTAGGGTTTCGATTTTAGGGTTT
1 -TTTAGGGTTT-GATTTTAGGGTTT
931711 GAAAGGCTTG
Statistics
Matches: 95, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
28 2 0.02
29 47 0.49
30 14 0.15
31 10 0.11
32 22 0.23
ACGTcount: A:0.21, C:0.01, G:0.33, T:0.45
Consensus pattern (29 bp):
TTTAGGGTTTGATTTTAGGGTTTAGAGAG
Found at i:931666 original size:16 final size:16
Alignment explanation
Indices: 931566--931696 Score: 71
Period size: 16 Copynumber: 8.6 Consensus size: 16
931556 GACTTTTGAT
* *
931566 TTTAGGGTTTTGA-AA
1 TTTAGGGTTTAGAGAG
* *
931581 TTTAGGGTTTGGAAAG
1 TTTAGGGTTTAGAGAG
* * *
931597 TTTAGGGTTTGGAAAT
1 TTTAGGGTTTAGAGAG
* *
931613 TTTAGGGTTTAAAGGG
1 TTTAGGGTTTAGAGAG
* * *
931629 TATGGGGTTT---GAT
1 TTTAGGGTTTAGAGAG
*
931642 TTTATGGTTTAGAGAG
1 TTTAGGGTTTAGAGAG
*
931658 TTTAGGGTTT--AG-T
1 TTTAGGGTTTAGAGAG
931671 TTTAGGGTTTAGAG-G
1 TTTAGGGTTTAGAGAG
931686 ATTTAGGGTTT
1 -TTTAGGGTTT
931697 CGATTTTAGG
Statistics
Matches: 90, Mismatches: 19, Indels: 13
0.74 0.16 0.11
Matches are distributed among these distances:
13 18 0.20
14 2 0.02
15 14 0.16
16 56 0.62
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (16 bp):
TTTAGGGTTTAGAGAG
Found at i:931667 original size:7 final size:7
Alignment explanation
Indices: 931642--931710 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 7
931632 GGGGTTTGAT
*
931642 TTTATGG
1 TTTAGGG
931649 TTTAGAGAG
1 TTTAG-G-G
931658 TTTAGGG
1 TTTAGGG
*
931665 TTTA-GT
1 TTTAGGG
931671 TTTAGGG
1 TTTAGGG
931678 TTTAGAGG
1 TTTAG-GG
931686 ATTTAGGG
1 -TTTAGGG
* **
931694 TTTCGAT
1 TTTAGGG
931701 TTTAGGG
1 TTTAGGG
931708 TTT
1 TTT
931711 GAAAGGCTTG
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
6 5 0.10
7 26 0.54
8 6 0.12
9 11 0.23
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:931726 original size:30 final size:28
Alignment explanation
Indices: 931611--931723 Score: 95
Period size: 29 Copynumber: 3.8 Consensus size: 28
931601 GGGTTTGGAA
931611 ATTTTAGGGTTTAAAGGGTATG-GGGTTTG
1 ATTTTAGGGTTTAAA-GGT-TGAGGGTTTG
* * *
931640 ATTTTATGGTTTAGAGAGTTTAGGGTTT-
1 ATTTTAGGGTTTAAAG-GTTGAGGGTTTG
* *
931668 AGTTTTAGGGTTTAGAGGATTTAGGGTTTCG
1 A-TTTTAGGGTTTAAAGG-TTGAGGGTTT-G
931699 ATTTTAGGGTTTGAAAGGCTTGAGG
1 ATTTTAGGGTTT-AAAGG-TTGAGG
931724 TTTAGTTAGT
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
28 4 0.06
29 45 0.64
30 11 0.16
31 10 0.14
ACGTcount: A:0.21, C:0.02, G:0.35, T:0.42
Consensus pattern (28 bp):
ATTTTAGGGTTTAAAGGTTGAGGGTTTG
Found at i:931727 original size:59 final size:58
Alignment explanation
Indices: 931612--931730 Score: 134
Period size: 58 Copynumber: 2.0 Consensus size: 58
931602 GGTTTGGAAA
* * * * *
931612 TTTTAGGGTTTAAAGGGTATGGGGTTTGATTTTATGGTTTAGAGAGTTTAGGGTTTAG
1 TTTTAGGGTTTAAAGGATATAGGGTTTGATTTTAGGGTTTAAAGAGTTGAGGGTTTAG
* *
931670 TTTTAGGGTTTAGAGGATTTAGGGTTTCGATTTTAGGGTTTGAAAG-GCTTGA-GGTTTAG
1 TTTTAGGGTTTAAAGGATATAGGGTTT-GATTTTAGGGTTT-AAAGAG-TTGAGGGTTTAG
931729 TT
1 TT
931731 AGTTTTTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
58 23 0.45
59 22 0.43
60 6 0.12
ACGTcount: A:0.20, C:0.02, G:0.34, T:0.45
Consensus pattern (58 bp):
TTTTAGGGTTTAAAGGATATAGGGTTTGATTTTAGGGTTTAAAGAGTTGAGGGTTTAG
Found at i:932017 original size:20 final size:20
Alignment explanation
Indices: 931992--932037 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
931982 TACTAGTTAA
931992 TTTTATAATCATTT-TATATT
1 TTTTATAATCATTTAT-TATT
* *
932012 TTTTATTATTATTTATTATT
1 TTTTATAATCATTTATTATT
932032 TTTTAT
1 TTTTAT
932038 TTAACACTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATAATCATTTATTATT
Found at i:932026 original size:10 final size:10
Alignment explanation
Indices: 932003--932038 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
931993 TTTATAATCA
932003 TTTTA-TATT
1 TTTTATTATT
932012 TTTTATTATT
1 TTTTATTATT
*
932022 ATTTATTATT
1 TTTTATTATT
932032 TTTTATT
1 TTTTATT
932039 TAACACTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 5 0.21
10 19 0.79
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTATTATT
Found at i:932098 original size:3 final size:3
Alignment explanation
Indices: 932090--932135 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
932080 TTTTAAAATC
* * * *
932090 ATT ATT ATT ATT AAT ATT ATT ATC ATT ATT ATT GTC ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
932136 ATCATTATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:932127 original size:12 final size:12
Alignment explanation
Indices: 932087--932143 Score: 78
Period size: 12 Copynumber: 4.7 Consensus size: 12
932077 AAGTTTTAAA
932087 ATCATTATTATT
1 ATCATTATTATT
* *
932099 ATTAATATTATT
1 ATCATTATTATT
932111 ATCATTATTATT
1 ATCATTATTATT
*
932123 GTCATTATTATT
1 ATCATTATTATT
932135 AATCATTAT
1 -ATCATTAT
932144 AAAACAACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
12 31 0.82
13 7 0.18
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (12 bp):
ATCATTATTATT
Found at i:935490 original size:15 final size:16
Alignment explanation
Indices: 935462--935495 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
935452 GACATATGAT
935462 TAAATAATTAATTAAA
1 TAAATAATTAATTAAA
935478 TAAATAA-TAATTAAA
1 TAAATAATTAATTAAA
935493 TAA
1 TAA
935496 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAATAATTAATTAAA
Found at i:935507 original size:15 final size:14
Alignment explanation
Indices: 935455--935503 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
935445 AAAAAGTGAC
935455 ATATGATTAAATAAT
1 ATAT-ATTAAATAAT
935470 -TA-ATTAAATAA-
1 ATATATTAAATAAT
935481 ATAATAATTAAATAAT
1 AT-AT-ATTAAATAAT
935497 ATATATT
1 ATATATT
935504 TAAAATGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
12 10 0.34
13 1 0.03
14 5 0.17
15 11 0.38
16 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
ATATATTAAATAAT
Found at i:936620 original size:30 final size:30
Alignment explanation
Indices: 936584--936641 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
936574 AATAATTTAT
936584 ATTAAGGATTTATTT-AAGTACAAATTAATG
1 ATTAAGGATTTATTTGAA-TACAAATTAATG
*
936614 ATTAAGGATTTATTTGAATATAAATTAA
1 ATTAAGGATTTATTTGAATACAAATTAA
936642 AAGTTAAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (30 bp):
ATTAAGGATTTATTTGAATACAAATTAATG
Found at i:936687 original size:30 final size:30
Alignment explanation
Indices: 936622--936717 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
936612 TGATTAAGGA
* * *
936622 TTTATTTGAATATAAATTAAAAGTTAA-AGG
1 TTTATTTGAGTGTAAATTAAAATTTAAGA-G
*
936652 CTTATTTGAGTGTAAATTAAAATTTAAGAG
1 TTTATTTGAGTGTAAATTAAAATTTAAGAG
* * *
936682 TTTATTTGAGCGT-AATAAAAATATTAGGA-
1 TTTATTTGAGTGTAAATTAAAAT-TTAAGAG
936711 TTTATTT
1 TTTATTT
936718 AAATATAAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
29 15 0.27
30 40 0.71
31 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.43
Consensus pattern (30 bp):
TTTATTTGAGTGTAAATTAAAATTTAAGAG
Found at i:936930 original size:2 final size:2
Alignment explanation
Indices: 936925--936954 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
936915 CTCGACATCG
936925 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
936955 ATAACACGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:948185 original size:154 final size:153
Alignment explanation
Indices: 947905--948212 Score: 553
Period size: 154 Copynumber: 2.0 Consensus size: 153
947895 ATCGGAATCC
* *
947905 ATGGCATACATGAAAGAGAAAGCCGCAGATGACCAAAACACATCTTTCCCACATCGAAACATATT
1 ATGGCATACATGAAAGAGAAAGCCACAGATGACCAAAACACATCTTTCACACATCGAAACATATT
*
947970 AAGGTTGATAAAGGCATTTAACGCAGGAAACATACTAAATGATTTAAAAGTCCACAGAGAACAAT
66 AAGGCTGATAAAGGCATTTAACGCAGGAAACATACTAAATGATTTAAAAGTCCACAGAGAACAAT
948035 TTGCCCAAGCAAAAAAATTATGTA
131 TTGCCCAAGC-AAAAAATTATGTA
*
948059 ATGGCATACATGAAAGAGAAAGCCACAGATGACCAAAACACATCTTTCACACATCTAAACATATT
1 ATGGCATACATGAAAGAGAAAGCCACAGATGACCAAAACACATCTTTCACACATCGAAACATATT
*
948124 AAGGCTGATAAAGGCATTTAACGCAGGAAACATGCTAAATGATTTAAAAGTCCACAGAGAACAAT
66 AAGGCTGATAAAGGCATTTAACGCAGGAAACATACTAAATGATTTAAAAGTCCACAGAGAACAAT
*
948189 TTGCCCGAGCAAAAAATTATGTA
131 TTGCCCAAGCAAAAAATTATGTA
948212 A
1 A
948213 CCTGATACAC
Statistics
Matches: 148, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
153 14 0.09
154 134 0.91
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (153 bp):
ATGGCATACATGAAAGAGAAAGCCACAGATGACCAAAACACATCTTTCACACATCGAAACATATT
AAGGCTGATAAAGGCATTTAACGCAGGAAACATACTAAATGATTTAAAAGTCCACAGAGAACAAT
TTGCCCAAGCAAAAAATTATGTA
Found at i:952397 original size:2 final size:2
Alignment explanation
Indices: 952392--952416 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
952382 ACACAAGCAA
952392 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
952417 TAAAATGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:954669 original size:19 final size:19
Alignment explanation
Indices: 954645--954682 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
954635 ATAGGTTTGT
954645 TATTGTCTTTGAATTCATA
1 TATTGTCTTTGAATTCATA
954664 TATTGTCTTTGAATTCATA
1 TATTGTCTTTGAATTCATA
954683 CTGATAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (19 bp):
TATTGTCTTTGAATTCATA
Found at i:959878 original size:141 final size:141
Alignment explanation
Indices: 959640--959901 Score: 434
Period size: 141 Copynumber: 1.9 Consensus size: 141
959630 ATTAAAACAC
* * *
959640 ACATAGCACAACACAAATTAACAGGGAAAATAGTACCCTTTAATCTTAATTACTCAGAACTGGAA
1 ACATAACACAACACAAATTAACAGGGAAAAAAGTACCCTTTAATCTTAATTACCCAGAACTGGAA
* *
959705 TCTGGGACAAGAATAACATGGAAATCAACGAAAAACAAGAACACCCATCAACTAAAACCTTAAAC
66 TCTAGAACAAGAATAACATGGAAATCAACGAAAAACAAGAACACCCATCAACTAAAACCTTAAAC
959770 CCTTAAAGTAT
131 CCTTAAAGTAT
* * * *
959781 ACATAACACAACTCAAATTAACGGGGAAAAAAGTACCCTTTAATCTTAATTACCCAGAGCTGGAG
1 ACATAACACAACACAAATTAACAGGGAAAAAAGTACCCTTTAATCTTAATTACCCAGAACTGGAA
*
959846 TCTAGAACAAGAATAACATGGAAATCAACGAAAAACAAGAATACCCATCAACTAAA
66 TCTAGAACAAGAATAACATGGAAATCAACGAAAAACAAGAACACCCATCAACTAAA
959902 CCAGATGAAG
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
141 111 1.00
ACGTcount: A:0.47, C:0.21, G:0.13, T:0.19
Consensus pattern (141 bp):
ACATAACACAACACAAATTAACAGGGAAAAAAGTACCCTTTAATCTTAATTACCCAGAACTGGAA
TCTAGAACAAGAATAACATGGAAATCAACGAAAAACAAGAACACCCATCAACTAAAACCTTAAAC
CCTTAAAGTAT
Found at i:960707 original size:16 final size:16
Alignment explanation
Indices: 960686--960733 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
960676 CACATAATCT
960686 TTTAAATATTATATTA
1 TTTAAATATTATATTA
* * *
960702 TTTAAAAATTTTATAA
1 TTTAAATATTATATTA
*
960718 TTTAAATAATATATTA
1 TTTAAATATTATATTA
960734 ATTTTTTAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAATATTATATTA
Found at i:960795 original size:18 final size:18
Alignment explanation
Indices: 960701--960801 Score: 55
Period size: 19 Copynumber: 5.3 Consensus size: 18
960691 ATATTATATT
960701 ATTTAAAAATT-TT-ATA
1 ATTTAAAAATTATTAATA
*
960717 ATTTAAATAATATATTAATT
1 ATTTAAA-AAT-TATTAATA
*
960737 TTTTAAAAAATT-TTAATA
1 ATTT-AAAAATTATTAATA
** *
960755 CTATATTAAATCTTATATCATA
1 --AT-TTAAAAATTAT-TAATA
*
960777 ATTTAAAAATTATTCATA
1 ATTTAAAAATTATTAATA
960795 ATATTAA
1 AT-TTAA
960802 CATTTTTCAT
Statistics
Matches: 65, Mismatches: 9, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
16 7 0.11
17 3 0.05
18 13 0.20
19 16 0.25
20 16 0.25
21 6 0.09
22 4 0.06
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTTAAAAATTATTAATA
Found at i:961044 original size:10 final size:10
Alignment explanation
Indices: 961029--961053 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
961019 AATATAAAAA
961029 TATTTTAATT
1 TATTTTAATT
961039 TATTTTAATT
1 TATTTTAATT
961049 TATTT
1 TATTT
961054 AAAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTAATT
Found at i:961236 original size:38 final size:38
Alignment explanation
Indices: 961194--961310 Score: 109
Period size: 38 Copynumber: 3.1 Consensus size: 38
961184 GTCATATCTA
*
961194 ATCGTATTATTTATATATAAACATGTTAATCAAGTCAT
1 ATCGTATTATTTATATATAAACATGTTAATTAAGTCAT
* * *
961232 ATCGTATCATATTAT-T-TAAATA-ATTAATTATA-TC-T
1 ATCGTATTAT-TTATATATAAACATGTTAATTA-AGTCAT
* * *
961267 AATCGTGTTATTTATATATAATCATGTTAATTGAGTCAT
1 -ATCGTATTATTTATATATAAACATGTTAATTAAGTCAT
961306 ATCGT
1 ATCGT
961311 GTTGTGTTAT
Statistics
Matches: 61, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
35 5 0.08
36 17 0.28
37 11 0.18
38 23 0.38
39 5 0.08
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (38 bp):
ATCGTATTATTTATATATAAACATGTTAATTAAGTCAT
Found at i:961283 original size:19 final size:19
Alignment explanation
Indices: 961259--961295 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
961249 AAATAATTAA
* *
961259 TTATATCTAATCGTGTTAT
1 TTATATATAATCATGTTAT
961278 TTATATATAATCATGTTA
1 TTATATATAATCATGTTA
961296 ATTGAGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.51
Consensus pattern (19 bp):
TTATATATAATCATGTTAT
Found at i:961422 original size:17 final size:18
Alignment explanation
Indices: 961400--961438 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
961390 GTATCATATT
961400 TATATTTAAAT-TATTTA
1 TATATTTAAATATATTTA
*
961417 TATATTTATATCATATTTA
1 TATATTTAAAT-ATATTTA
961436 TAT
1 TAT
961439 CATTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
19 9 0.47
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTTAAATATATTTA
Found at i:961447 original size:11 final size:11
Alignment explanation
Indices: 961391--961441 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
961381 ATAATAAATG
961391 TATCATATTTA
1 TATCATATTTA
* * *
961402 TATTTAAATTATT
1 TA-TCATATT-TA
961415 TAT-ATATTTA
1 TATCATATTTA
961425 TATCATATTTA
1 TATCATATTTA
961436 TATCAT
1 TATCAT
961442 TATTATTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
10 4 0.12
11 19 0.59
12 6 0.19
13 3 0.09
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (11 bp):
TATCATATTTA
Found at i:963921 original size:2 final size:2
Alignment explanation
Indices: 963914--963951 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
963904 ATGCATTTCT
* *
963914 TA TA TA TA TA TA TA TA TA T- TA TA TA TT TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
963952 GTTTTATTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:963937 original size:19 final size:19
Alignment explanation
Indices: 963913--963951 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
963903 AATGCATTTC
963913 TTATATATATATATATATA
1 TTATATATATATATATATA
* *
963932 TTATATATTTATATTTATA
1 TTATATATATATATATATA
963951 T
1 T
963952 GTTTTATTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATATATATATATATATA
Found at i:971371 original size:15 final size:15
Alignment explanation
Indices: 971353--971393 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
971343 TAACAATCAT
971353 AATTATAAATATTAA
1 AATTATAAATATTAA
971368 AATT-TAAATA-TAA
1 AATTATAAATATTAA
*
971381 AGTTATTAAATAT
1 AATTA-TAAATAT
971394 CAATTTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
13 6 0.27
14 6 0.27
15 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
AATTATAAATATTAA
Found at i:977548 original size:24 final size:23
Alignment explanation
Indices: 977496--977548 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
977486 TTTGATAACG
*
977496 TTAAAAAAAATTATAATTATGA-
1 TTAAAAAAAATTATAATTATAAT
977518 TTAAAAAAATTATTATAACTT-TAAT
1 TTAAAAAAA--ATTATAA-TTATAAT
977543 TTAAAA
1 TTAAAA
977549 TTTTTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 9 0.35
24 9 0.35
25 8 0.31
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TTAAAAAAAATTATAATTATAAT
Found at i:979928 original size:36 final size:36
Alignment explanation
Indices: 979769--979933 Score: 143
Period size: 36 Copynumber: 4.6 Consensus size: 36
979759 GTTGTTGATG
* * * *
979769 GATTAAGTAGATATGAGCGCTTGTTAGTAATTAACA
1 GATTAAGTAGTTCTGAGCACGTGTTAGTAATTAACA
* * *
979805 GATTGAGTAGTTCTGAGCATGTGTTAGTAATTAAATA
1 GATTAAGTAGTTCTGAGCACGTGTTAGTAATT-AACA
* * * * * * *
979842 AATTAAGTGGATATGAGAATGCT-TTAGTAATTAACG
1 GATTAAGTAGTTCTGAGCACG-TGTTAGTAATTAACA
** *
979878 GATTGTGTAGTTCTGAGCACGTGTTAGTAATTAACG
1 GATTAAGTAGTTCTGAGCACGTGTTAGTAATTAACA
*
979914 GATTAAGTACTTCTGAGCAC
1 GATTAAGTAGTTCTGAGCAC
979934 ATGAACATGT
Statistics
Matches: 100, Mismatches: 26, Indels: 6
0.76 0.20 0.05
Matches are distributed among these distances:
35 1 0.01
36 71 0.71
37 27 0.27
38 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.35
Consensus pattern (36 bp):
GATTAAGTAGTTCTGAGCACGTGTTAGTAATTAACA
Found at i:984772 original size:17 final size:16
Alignment explanation
Indices: 984733--984779 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
984723 TTGTCTTAGT
984733 TTTATATTT-CTTTT-
1 TTTATATTTACTTTTA
984747 TTT-TATTTACTTTTA
1 TTTATATTTACTTTTA
*
984762 TATTATATTTACTATTA
1 T-TTATATTTACTTTTA
984779 T
1 T
984780 CAATTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.18
14 8 0.29
15 1 0.04
16 2 0.07
17 12 0.43
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATATTTACTTTTA
Found at i:986387 original size:94 final size:95
Alignment explanation
Indices: 986225--986415 Score: 303
Period size: 94 Copynumber: 2.0 Consensus size: 95
986215 ATTGATGCAT
* * *
986225 CTAAGTAAAAAAAGAAACATATTTATAGTTTATCAAGCTAATTTATGTCAGATTCATCCAAAATC
1 CTAAGTAAAAAAAGAAACATACTTATAATTTATCAAGCTAATATATGTCAGATTCATCCAAAATC
*
986290 TGACATGACAAGGGCTAATAGATATCATTG
66 TGACATGACAAGGGCTAACAGATATCATTG
**
986320 CTAAGT-AAAAAAGAAATGTACTTATAATTTATCAAGCTAATATATGTCAGATTCATCCAAAATC
1 CTAAGTAAAAAAAGAAACATACTTATAATTTATCAAGCTAATATATGTCAGATTCATCCAAAATC
* *
986384 TGACATGATAAGGGCTAACAGATGTCATTG
66 TGACATGACAAGGGCTAACAGATATCATTG
986414 CT
1 CT
986416 CATTGTTATT
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 82 0.93
95 6 0.07
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (95 bp):
CTAAGTAAAAAAAGAAACATACTTATAATTTATCAAGCTAATATATGTCAGATTCATCCAAAATC
TGACATGACAAGGGCTAACAGATATCATTG
Found at i:988212 original size:44 final size:44
Alignment explanation
Indices: 988162--988250 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
988152 AATGGAGAAG
* *
988162 AAAGCATTTAGTCTGCAGCTAACTAGAGAGAAAAAATTGTAAAT
1 AAAGCATTTAGTCTGCAGCCAACTAGAGAGAAAAAAATGTAAAT
**
988206 AAAGCATTTAGTCTGCAGCCATGTAGAGAGAAAAAAATGTAAAT
1 AAAGCATTTAGTCTGCAGCCAACTAGAGAGAAAAAAATGTAAAT
988250 A
1 A
988251 GGATATGAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (44 bp):
AAAGCATTTAGTCTGCAGCCAACTAGAGAGAAAAAAATGTAAAT
Found at i:997424 original size:22 final size:22
Alignment explanation
Indices: 997382--997425 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
997372 TTATTACAAC
*
997382 TTTTAAAAATATTTTTAATATT
1 TTTTAAAAATATCTTTAATATT
*
997404 TTTTATAAATAATCTTT-ATATT
1 TTTTAAAAAT-ATCTTTAATATT
997426 ATCTTCAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTAAAAATATCTTTAATATT
Found at i:998973 original size:65 final size:58
Alignment explanation
Indices: 998904--999187 Score: 160
Period size: 65 Copynumber: 4.6 Consensus size: 58
998894 TTATTCAAGG
*
998904 AAAATTGATACTTTCAACTTTTCCTCAAAAATATCCTTTTTTTATTGAAAATTTATTTTTTAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATA----TTTTTT-TTGAAAA-TT-TTATTTAAAA
* * *
998969 AAAATTGATATTTTCAACTTTTTCTTAAAAATATTTTTTTTGAAAATTTTATTTAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTTATTTAAAA
* * * * * * * * * *** *
999027 AAAATTAAAATTTTTAACTTTTCTTTAACAATGTTTTTTAAATTTTTATTTTTTTATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAA-AA-ATATTTT---TTTTGAAAATTTTA-TTT-AAAA
* * ** * *
999092 AAAATTGATACTTTCAACTTTTTCTTAAAAAATATATTTTTTAAAAAATTTGATTTTCAAAG
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATAT-TTTTTTTGAAAATTTTA-TTT-AAAA
* *
999154 AAAATTTATAC-TTCAAC-TTTCCT-TAAAATATTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTT
999188 AAAAATTTTT
Statistics
Matches: 176, Mismatches: 34, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
57 3 0.02
58 39 0.22
59 9 0.05
60 12 0.07
61 12 0.07
62 25 0.14
63 10 0.06
64 5 0.03
65 52 0.30
66 9 0.05
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTTATTTAAAA
Found at i:999046 original size:58 final size:56
Alignment explanation
Indices: 998941--999077 Score: 150
Period size: 58 Copynumber: 2.4 Consensus size: 56
998931 AAAATATCCT
* * *
998941 TTTTTTATTGAAAATTTATTTTTTAAAAAAAATTGATATTTTCAACTTTTTCTTAAAAATA
1 TTTTTT-TTGAAAA-TT-TTATTTAAAAAAAATTAAAATTTTCAAC-TTTTCTTAAAAA-A
* * *
999002 TTTTTTTTGAAAATTTTATTTAAAAAAAATTAAAATTTTTAACTTTTCTTTAACAA
1 TTTTTTTTGAAAATTTTATTTAAAAAAAATTAAAATTTTCAACTTTTCTTAAAAAA
* *
999058 TGTTTTTT-AAATTTTTATTT
1 TTTTTTTTGAAAATTTTATTT
999078 TTTTATTTTC
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
55 11 0.16
56 8 0.12
57 10 0.15
58 24 0.35
59 2 0.03
60 7 0.10
61 6 0.09
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.55
Consensus pattern (56 bp):
TTTTTTTTGAAAATTTTATTTAAAAAAAATTAAAATTTTCAACTTTTCTTAAAAAA
Found at i:999198 original size:124 final size:121
Alignment explanation
Indices: 998966--999256 Score: 342
Period size: 123 Copynumber: 2.4 Consensus size: 121
998956 TTATTTTTTA
* ** *
998966 AAAAAAATTGATATTTTCAACTTTTTCTT-AAAAATATTTTTTTTGAAAATTTTATTTAAAAAAA
1 AAAAAAATTGATACTTTCAACTTTTTCTTAAAAAATATTTTTTTAAAAAATTTGATTTAAAAAAA
* * * * **
999030 ATTAAAATTTTTAACTTTTCTTTAACAATGTTTTTTAAATTTTTATTTTTTTATTTTC
66 ATTAAAATCTTCAACTTTTCCTTAACAATATTTTAAAAATTTTTA-TTTTTTA-TTTC
999088 AAGAAAAATTGATACTTTCAACTTTTTCTTAAAAAATATATTTTTTAAAAAATTTGATTTTCAAA
1 AA-AAAAATTGATACTTTCAACTTTTTCTTAAAAAATAT-TTTTTTAAAAAATTTGA-TTT-AAA
* * *
999153 GAAAATTTATA-CTTCAAC-TTTCCTTAA-AATATTTTAAAAATTTTTATTTTTTATTTC
62 AAAAATTAAAATCTTCAACTTTTCCTTAACAATATTTTAAAAATTTTTATTTTTTATTTC
* *
999210 AAAAAAA-TGATACTTTTAA-TTTGTTCTTACAAAATATTTTTTTAAAA
1 AAAAAAATTGATACTTTCAACTTT-TTCTTAAAAAATATTTTTTTAAAA
999257 TTTTATTTTT
Statistics
Matches: 148, Mismatches: 15, Indels: 15
0.83 0.08 0.08
Matches are distributed among these distances:
119 13 0.09
120 24 0.16
121 5 0.03
122 8 0.05
123 33 0.22
124 24 0.16
125 22 0.15
126 8 0.05
127 11 0.07
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (121 bp):
AAAAAAATTGATACTTTCAACTTTTTCTTAAAAAATATTTTTTTAAAAAATTTGATTTAAAAAAA
ATTAAAATCTTCAACTTTTCCTTAACAATATTTTAAAAATTTTTATTTTTTATTTC
Found at i:999325 original size:3 final size:3
Alignment explanation
Indices: 999319--999349 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
999309 AATAATAGAC
999319 ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
999350 GAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:999356 original size:14 final size:14
Alignment explanation
Indices: 999319--999349 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
999309 AATAATAGAC
999319 ATAATAATAATAATA
1 ATAATAA-AATAATA
999334 ATAATAAAATAATA
1 ATAATAAAATAATA
999348 AT
1 AT
999350 GAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATAAAATAATA
Found at i:1000540 original size:43 final size:45
Alignment explanation
Indices: 1000358--1000595 Score: 217
Period size: 44 Copynumber: 5.4 Consensus size: 45
1000348 GCCGAGATTC
* * * * *
1000358 ACAA-TTTCTGAAGAATAAACAAAACTTTTCTAAA-CGGAGGCTTA
1 ACAACTTT-TGAAAAATAAACAAAGCTTCTCTAAATCAGAGGCTCA
* *
1000402 ACAA-TTTCAGAAAAATAAACAAGGC-TCTTCT-AATCAGAGGCTCA
1 ACAACTTT-TGAAAAATAAACAAAGCTTC-TCTAAATCAGAGGCTCA
* * *
1000446 ACAACTTTTAAAAAATAAACAAAGGTTCCTCTAAA-CAGAAGCTCA
1 ACAACTTTTGAAAAATAAACAAAGCTT-CTCTAAATCAGAGGCTCA
*
1000491 ACAAC-TTTGAAAAATAAATAAAGCTTCTCTAAAT-AGAGGCTCA
1 ACAACTTTTGAAAAATAAACAAAGCTTCTCTAAATCAGAGGCTCA
* * * * *
1000534 ATAACTTTT-AAAAATAAACAAAGCTCCT-TTAATCAGAGGCACC
1 ACAACTTTTGAAAAATAAACAAAGCTTCTCTAAATCAGAGGCTCA
*
1000577 ATAACTTTTGAAAAATAAA
1 ACAACTTTTGAAAAATAAA
1000596 TTACTCCTTT
Statistics
Matches: 162, Mismatches: 22, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
42 4 0.02
43 55 0.34
44 79 0.49
45 21 0.13
46 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (45 bp):
ACAACTTTTGAAAAATAAACAAAGCTTCTCTAAATCAGAGGCTCA
Found at i:1000615 original size:42 final size:43
Alignment explanation
Indices: 1000496--1000679 Score: 173
Period size: 43 Copynumber: 4.3 Consensus size: 43
1000486 GCTCAACAAC
* * * *
1000496 TTTGAAAAATAAATAAAGCTTCTCTAAATAGAGGCTCAATAACT
1 TTTGAAAAATAAAT-AAGCTCCTTTAAATAGAGGCACCATAACT
*
1000540 TTT-AAAAATAAACAAAGCTCCTTT-AATCAGAGGCACCATAACT
1 TTTGAAAAATAAA-TAAGCTCCTTTAAAT-AGAGGCACCATAACT
* *
1000583 TTTGAAAAATAAATTA-CTCCTTTAAATAGAGGCACCACAACTT
1 TTTGAAAAATAAATAAGCTCCTTTAAATAGAGGCACCATAAC-T
* * * * *
1000626 TTTAAAAAATAAAT-TG-TTCTTCTAAACAGAGGTACCATAACT
1 TTTGAAAAATAAATAAGCTCCTT-TAAATAGAGGCACCATAACT
1000668 TTTG-AAAATAAA
1 TTTGAAAAATAAA
1000680 ACGCTTATCG
Statistics
Matches: 118, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
41 8 0.07
42 31 0.26
43 67 0.57
44 12 0.10
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.30
Consensus pattern (43 bp):
TTTGAAAAATAAATAAGCTCCTTTAAATAGAGGCACCATAACT
Found at i:1000931 original size:21 final size:22
Alignment explanation
Indices: 1000907--1000956 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1000897 ACGTCCAACA
* *
1000907 TTTAAAGATTCTCATTC-AAAT
1 TTTAAAGATTCTCATCCAAAAG
*
1000928 TTTAGAGATTCTCATCCAAAAG
1 TTTAAAGATTCTCATCCAAAAG
1000950 TTTAAAG
1 TTTAAAG
1000957 CTTTTCGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (22 bp):
TTTAAAGATTCTCATCCAAAAG
Found at i:1001080 original size:114 final size:114
Alignment explanation
Indices: 1000948--1001217 Score: 380
Period size: 114 Copynumber: 2.4 Consensus size: 114
1000938 CTCATCCAAA
* *
1000948 AGTTTAAAGCTTTTCGTTTGAATTTAAAAGGTTCACATTCAAGAAATCTTAGAGTTTCACATCTA
1 AGTTTAAAGCTTTTCGTTTGAATTTAAAAGATTCACATCCAAGAAATCTTAGAGTTTCACATCTA
* * * * *
1001013 AGTTCAAAGGTAT-TCACTCAAAAATTTAGAGATTCGCTTTCAAAAGTTG
66 AGTTCAAAAGT-TCTCACTCAAAAATTTAGAGATCCGCATCCAAAAATTG
* ***
1001062 AGTTCAAAGCTTTTCGTTTGAATTTTGGAGATTCACATCCAAGAAATCTTAGAGTTTCACATCTA
1 AGTTTAAAGCTTTTCGTTTGAATTTAAAAGATTCACATCCAAGAAATCTTAGAGTTTCACATCTA
*
1001127 AGTTCAAAAGTTCTCACTCAAAAATTTAGAGATCCGCATCCAAAAATTT
66 AGTTCAAAAGTTCTCACTCAAAAATTTAGAGATCCGCATCCAAAAATTG
** * *
1001176 AGTTTAAAGCTTTTTTTTTGAATTTTAGAGATTCACATCCAA
1 AGTTTAAAGCTTTTCGTTTGAATTTAAAAGATTCACATCCAA
1001218 AAGTTTAAAA
Statistics
Matches: 139, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
113 1 0.01
114 138 0.99
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (114 bp):
AGTTTAAAGCTTTTCGTTTGAATTTAAAAGATTCACATCCAAGAAATCTTAGAGTTTCACATCTA
AGTTCAAAAGTTCTCACTCAAAAATTTAGAGATCCGCATCCAAAAATTG
Found at i:1001304 original size:21 final size:21
Alignment explanation
Indices: 1001279--1001318 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1001269 GTTTCACATC
1001279 TCAAAAATTCTCATTTGAAAT
1 TCAAAAATTCTCATTTGAAAT
*
1001300 TCAAATATTCTCATTTGAA
1 TCAAAAATTCTCATTTGAA
1001319 TTTGAAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (21 bp):
TCAAAAATTCTCATTTGAAAT
Found at i:1001372 original size:79 final size:78
Alignment explanation
Indices: 1001259--1001554 Score: 421
Period size: 79 Copynumber: 3.7 Consensus size: 78
1001249 CACACCCAAC
* *
1001259 AAATTTTGAGGTTTCACATCTCAAAAATTCTCATTTGAAATTCAAATATTCTCATTTGAATTTGA
1 AAATTTT-A-GTTTCACACCTCAAAGATTCTCATTTGAAATTCAAATATTCTCATTTGAATTTGA
*
1001324 AGATTTACATTCGAT
64 AGATTCACATTCGAT
* * * *
1001339 AAATTTTATGATTCACACCTCAAATATTTTCATTTGAAATTCAATTATTCTCATTTGAATTTGAA
1 AAATTTTA-GTTTCACACCTCAAAGATTCTCATTTGAAATTCAAATATTCTCATTTGAATTTGAA
1001404 GATTCACATTCGAT
65 GATTCACATTCGAT
** * *
1001418 AAATTTTGAGTTTCACACCTCACGGATTCTCATTTGAAATTCAAAGATTCTCATTTGAATTCGAA
1 AAATTTT-AGTTTCACACCTCAAAGATTCTCATTTGAAATTCAAATATTCTCATTTGAATTTGAA
1001483 GATTCACATTCGAT
65 GATTCACATTCGAT
* * *
1001497 AAATTTTGGGTTTCACACCTTAAAGATTCTCATTTGAAATTTAAATATTCTCATTTGA
1 AAATTTT-AGTTTCACACCTCAAAGATTCTCATTTGAAATTCAAATATTCTCATTTGA
1001555 CACTCAAAGA
Statistics
Matches: 194, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
79 186 0.96
80 8 0.04
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (78 bp):
AAATTTTAGTTTCACACCTCAAAGATTCTCATTTGAAATTCAAATATTCTCATTTGAATTTGAAG
ATTCACATTCGAT
Found at i:1001382 original size:21 final size:21
Alignment explanation
Indices: 1001358--1001397 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1001348 GATTCACACC
*
1001358 TCAAATATTTTCATTTGAAAT
1 TCAAATATTCTCATTTGAAAT
*
1001379 TCAATTATTCTCATTTGAA
1 TCAAATATTCTCATTTGAA
1001398 TTTGAAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.47
Consensus pattern (21 bp):
TCAAATATTCTCATTTGAAAT
Found at i:1001468 original size:21 final size:20
Alignment explanation
Indices: 1001442--1001634 Score: 130
Period size: 21 Copynumber: 9.5 Consensus size: 20
1001432 ACACCTCACG
1001442 GATTCTCATTTGAAATTCAAA
1 GATTCTCATTTG-AATTCAAA
*
1001463 GATTCTCATTTGAATTCGAA
1 GATTCTCATTTGAATTCAAA
* *
1001483 GATTCACATTCG-A-T--AA
1 GATTCTCATTTGAATTCAAA
* ** *
1001499 -ATTTTGGGTTTCACACCTT-AAA
1 GATTCT-CATTTGA-A--TTCAAA
*
1001521 GATTCTCATTTGAAATTTAAA
1 GATTCTCATTTG-AATTCAAA
* *
1001542 TATTCTCATTTGACACTCAAA
1 GATTCTCATTTGA-ATTCAAA
1001563 GATTCTCATTTGACACTT-AAA
1 GATTCTCATTTGA-A-TTCAAA
*
1001584 GATTCTCATTTAAAATTCAAA
1 GATTCTCATTT-GAATTCAAA
1001605 GATTCTCATTTGAATTCAAA
1 GATTCTCATTTGAATTCAAA
* *
1001625 AATTCACATT
1 GATTCTCATT
1001635 CGATAAATTT
Statistics
Matches: 136, Mismatches: 22, Indels: 29
0.73 0.12 0.16
Matches are distributed among these distances:
15 3 0.02
16 4 0.03
18 2 0.01
19 1 0.01
20 38 0.28
21 75 0.55
22 8 0.06
23 5 0.04
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (20 bp):
GATTCTCATTTGAATTCAAA
Found at i:1001484 original size:20 final size:21
Alignment explanation
Indices: 1001442--1001492 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
1001432 ACACCTCACG
1001442 GATTCTCATTTGAAATTCAAA
1 GATTCTCATTTGAAATTCAAA
*
1001463 GATTCTCATTTG-AATTCGAA
1 GATTCTCATTTGAAATTCAAA
*
1001483 GATTCACATT
1 GATTCTCATT
1001493 CGATAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (21 bp):
GATTCTCATTTGAAATTCAAA
Found at i:1001565 original size:42 final size:42
Alignment explanation
Indices: 1001518--1001618 Score: 148
Period size: 42 Copynumber: 2.4 Consensus size: 42
1001508 TTCACACCTT
* * * *
1001518 AAAGATTCTCATTTGAAATTTAAATATTCTCATTTGACACTC
1 AAAGATTCTCATTTGAAACTTAAAGATTCTCATTTAAAACTC
* *
1001560 AAAGATTCTCATTTGACACTTAAAGATTCTCATTTAAAATTC
1 AAAGATTCTCATTTGAAACTTAAAGATTCTCATTTAAAACTC
1001602 AAAGATTCTCATTTGAA
1 AAAGATTCTCATTTGAA
1001619 TTCAAAAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.39
Consensus pattern (42 bp):
AAAGATTCTCATTTGAAACTTAAAGATTCTCATTTAAAACTC
Found at i:1001614 original size:63 final size:62
Alignment explanation
Indices: 1001515--1001634 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 62
1001505 GGTTTCACAC
* * * * *
1001515 CTTAAAGATTCTCATTTGAAATTTAAATATTCTCATTTGACACTCAAAGATTCTCATTTGACA
1 CTTAAAGATTCTCATTTAAAATTCAAAGATTCTCATTTGA-ACTCAAAAATTCACATTTGACA
*
1001578 CTTAAAGATTCTCATTTAAAATTCAAAGATTCTCATTTGAATTCAAAAATTCACATT
1 CTTAAAGATTCTCATTTAAAATTCAAAGATTCTCATTTGAACTCAAAAATTCACATT
1001635 CGATAAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
62 14 0.27
63 37 0.73
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.39
Consensus pattern (62 bp):
CTTAAAGATTCTCATTTAAAATTCAAAGATTCTCATTTGAACTCAAAAATTCACATTTGACA
Found at i:1002752 original size:18 final size:18
Alignment explanation
Indices: 1002731--1002774 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1002721 CTTAAGTTTT
1002731 TCTTTTCTC-TTCTTTTCA
1 TCTTTTCTCATTC-TTTCA
*
1002749 TCTTTTTTCATTCTTTCA
1 TCTTTTCTCATTCTTTCA
1002767 TCTTTTCT
1 TCTTTTCT
1002775 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68
Consensus pattern (18 bp):
TCTTTTCTCATTCTTTCA
Found at i:1002770 original size:26 final size:26
Alignment explanation
Indices: 1002741--1002805 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
1002731 TCTTTTCTCT
1002741 TCTTTTCATCTTTTTTCATTCTTTCA
1 TCTTTTCATCTTTTTTCATTCTTTCA
* * ** *
1002767 TCTTTTCTTTTTTTTTTTTTTTTTCA
1 TCTTTTCATCTTTTTTCATTCTTTCA
1002793 T-TTTTCATCTTTT
1 TCTTTTCATCTTTT
1002806 CCATCCATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 10 0.31
26 22 0.69
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (26 bp):
TCTTTTCATCTTTTTTCATTCTTTCA
Found at i:1006857 original size:58 final size:57
Alignment explanation
Indices: 1006794--1007097 Score: 245
Period size: 58 Copynumber: 5.0 Consensus size: 57
1006784 GTTTTTTAAA
*
1006794 ATTTTTATTTTTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCTTTAAAAAT
1 ATTTTTTTTTTTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCTTTAAAAAT
** * * * * *
1006851 ATTTTTTTTAAATTTGATTTTCAAGGAAAATTAATACTTACAACTTTTCCTTAAAAATATGTTT
1 ATTTTTTTT-TTTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTT-CTTTAAAA-A----T
* * *
1006915 ATAAAATTTTTTATTTTTTTATTTT-AAAAGAAAATTGATACTTTTAACTTTTCCTTAAAAAT
1 AT----TTTTTT-TTTTTTTATTTTCAAGA-AAAATTGATACTTTCAACTTTTCTTTAAAAAT
*** * * *
1006977 ATTTTTTTAAAATTTGATTTTCAA-AGAAAATTGATACGTTCAA-TTTTGTCTTAAAAAT
1 ATTTTTTT-TTTTTTTATTTTCAAGA-AAAATTGATACTTTCAACTTTTCT-TTAAAAAT
*
1007035 ATGTTTTTTAATTTTTTTTATTTTCAAGAAAAATTGATACTTTTAACTTTTCTTTAAAAAT
1 A--TTTTTT--TTTTTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCTTTAAAAAT
1007096 AT
1 AT
1007098 ATATTTTTGA
Statistics
Matches: 193, Mismatches: 33, Indels: 40
0.73 0.12 0.15
Matches are distributed among these distances:
57 12 0.06
58 73 0.38
59 10 0.05
60 7 0.04
61 35 0.18
62 10 0.05
64 3 0.02
66 1 0.01
67 8 0.04
68 33 0.17
69 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (57 bp):
ATTTTTTTTTTTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCTTTAAAAAT
Found at i:1006925 original size:68 final size:69
Alignment explanation
Indices: 1006853--1006991 Score: 174
Period size: 68 Copynumber: 2.0 Consensus size: 69
1006843 TTAAAAATAT
* *
1006853 TTTTTTTA-AATTTGATTTTCAAGGAAAATTAATACTTACAACTTTTCCTTAAAAATATGTTTAT
1 TTTTTTTATAATTTGATTTTAAAAGAAAATTAATACTTACAACTTTTCCTTAAAAATATGTTTAT
1006917 AAAA
66 AAAA
** * * ** * *
1006921 -TTTTTTATTTTTTTATTTTAAAAGAAAATTGATACTTTTAACTTTTCCTTAAAAATATTTTTTT
1 TTTTTTTATAATTTGATTTTAAAAGAAAATTAATACTTACAACTTTTCCTTAAAAATATGTTTAT
1006985 AAAA
66 AAAA
1006989 TTT
1 TTT
1006992 GATTTTCAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
67 7 0.12
68 50 0.85
69 2 0.03
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (69 bp):
TTTTTTTATAATTTGATTTTAAAAGAAAATTAATACTTACAACTTTTCCTTAAAAATATGTTTAT
AAAA
Found at i:1006955 original size:126 final size:124
Alignment explanation
Indices: 1006678--1007129 Score: 523
Period size: 126 Copynumber: 3.6 Consensus size: 124
1006668 TTTTTGAAAA
* * *
1006678 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTT-TCTTAAAATTTTTTTTTTTGAAAATTTT
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCT-TTAAAAATATTTTTTTT--AAATTTG
* * * *
1006742 ATTTTCAAGAAAAATTAATACTTTCAACTTTTTCC-TAACAATGTTTTTTAAAA-TTTTTATTTT
63 ATTTTCAAGGAAAATTAATAC-TTCAAC-TTTTCCTTAAAAATATGTTTTAAAATTTTTTA-TTT
1006805 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCTTTAAAAATATTTTTTTTAAATTTGATT
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCTTTAAAAATATTTTTTTTAAATTTGATT
1006870 TTCAAGGAAAATTAATACTTACAACTTTTCCTTAAAAATATGTTTATAAAATTTTTTATTT
66 TTCAAGGAAAATTAATACTT-CAACTTTTCCTTAAAAATATGTTT-TAAAATTTTTTATTT
* * * *
1006931 TTTTATTTT-AAAAGAAAATTGATACTTTTAACTTTTCCTTAAAAATATTTTTTTAAAATTTGAT
1 TTTTATTTTCAAGA-AAAATTGATACTTTCAACTTTTCTTTAAAAATATTTTTTTTAAATTTGAT
* * * **
1006995 TTTCAAAGAAAATTGATACGTTCAA-TTTTGTCTTAAAAATATG-TTT----TTTAAT-TTT
65 TTTCAAGGAAAATTAATAC-TTCAACTTTT-CCTTAAAAATATGTTTTAAAATTTTTTATTT
* * *
1007050 TTTTATTTTCAAGAAAAATTGATACTTTTAACTTTTCTTTAAAAATATATATTTTTGAAATTTTA
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCTTTAAAAATAT-T-TTTTTTAAATTTGA
*
1007115 TTTTTAA-GAAAATTA
64 TTTTCAAGGAAAATTA
1007130 TTAAAAAATA
Statistics
Matches: 292, Mismatches: 22, Indels: 29
0.85 0.06 0.08
Matches are distributed among these distances:
119 45 0.15
120 15 0.05
121 18 0.06
124 9 0.03
125 49 0.17
126 96 0.33
127 59 0.20
128 1 0.00
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (124 bp):
TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCTTTAAAAATATTTTTTTTAAATTTGATT
TTCAAGGAAAATTAATACTTCAACTTTTCCTTAAAAATATGTTTTAAAATTTTTTATTT
Found at i:1007173 original size:4 final size:4
Alignment explanation
Indices: 1007164--1007224 Score: 54
Period size: 4 Copynumber: 14.5 Consensus size: 4
1007154 CAATTTAATC
1007164 AATA AATA AATA GACATA AAT- AAT- AATAA CAATA AATA ATATA AATA
1 AATA AATA AATA -A-ATA AATA AATA AAT-A -AATA AATA A-ATA AATA
*
1007211 AATA TATA AATA AA
1 AATA AATA AATA AA
1007225 ATGAAAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
3 6 0.12
4 30 0.61
5 7 0.14
6 6 0.12
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:1007217 original size:12 final size:13
Alignment explanation
Indices: 1007165--1007224 Score: 72
Period size: 13 Copynumber: 4.7 Consensus size: 13
1007155 AATTTAATCA
*
1007165 ATAAATAAATAGAC
1 ATAAATAAATA-AT
1007179 ATAAAT-AATAAT
1 ATAAATAAATAAT
1007191 A-ACAATAAATAAT
1 ATA-AATAAATAAT
1007204 ATAAATAAAT-AT
1 ATAAATAAATAAT
1007216 ATAAATAAA
1 ATAAATAAA
1007225 ATGAAAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
11 1 0.02
12 16 0.38
13 18 0.43
14 7 0.17
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:1017241 original size:12 final size:12
Alignment explanation
Indices: 1017226--1017251 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1017216 AACAACTAGC
1017226 AAAAACAATAAT
1 AAAAACAATAAT
1017238 AAAAACAATAAT
1 AAAAACAATAAT
1017250 AA
1 AA
1017252 GAAGTCTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAACAATAAT
Found at i:1019034 original size:17 final size:17
Alignment explanation
Indices: 1019012--1019049 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1019002 CAAAATAGGT
*
1019012 AATTTTAAATTTATTCA
1 AATTTTAAAATTATTCA
*
1019029 AATTTTAAAATTATTTA
1 AATTTTAAAATTATTCA
1019046 AATT
1 AATT
1019050 AAAATTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTTAAAATTATTCA
Found at i:1025434 original size:42 final size:42
Alignment explanation
Indices: 1025375--1025459 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
1025365 GCAAGTAAAA
1025375 TCATAAGGAATTGGATTTAGGGTTTCCCTTGTTTTTCCTATT
1 TCATAAGGAATTGGATTTAGGGTTTCCCTTGTTTTTCCTATT
1025417 TCATAAGGAATTGGATTTAGGGTTTCCCTTGTTTTTCCTATT
1 TCATAAGGAATTGGATTTAGGGTTTCCCTTGTTTTTCCTATT
1025459 T
1 T
1025460 TAACACTATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (42 bp):
TCATAAGGAATTGGATTTAGGGTTTCCCTTGTTTTTCCTATT
Found at i:1028695 original size:10 final size:10
Alignment explanation
Indices: 1028669--1028698 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1028659 GAAACACGTG
*
1028669 ATATATATAT
1 ATATATTTAT
1028679 ATATATTTAT
1 ATATATTTAT
1028689 ATATATTTAT
1 ATATATTTAT
1028699 TGAGTAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATATATTTAT
Found at i:1031199 original size:17 final size:17
Alignment explanation
Indices: 1031179--1031212 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
1031169 AGGGGGAAAC
1031179 AAAAGTAAAAAAGAAAGA
1 AAAAG-AAAAAAGAAAGA
1031197 AAAAGAAAAAAGAAAG
1 AAAAGAAAAAAGAAAG
1031213 GGAAAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAGA
Found at i:1031634 original size:20 final size:21
Alignment explanation
Indices: 1031596--1031634 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1031586 GGCTTCTTTA
* *
1031596 ATTCGTTTTCTTTATATCATT
1 ATTCATTTTCTTTAGATCATT
1031617 ATTCATTTT-TTTAGATCA
1 ATTCATTTTCTTTAGATCA
1031635 GAATTCATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.23, C:0.13, G:0.05, T:0.59
Consensus pattern (21 bp):
ATTCATTTTCTTTAGATCATT
Found at i:1037808 original size:204 final size:202
Alignment explanation
Indices: 1037448--1037851 Score: 529
Period size: 204 Copynumber: 2.0 Consensus size: 202
1037438 AATTTCAAAC
* * ** *
1037448 AAATCACTTATGAGATTTGAGTCACTATTTTGAATAATCTTCACATTGACTCAAATTTCATCATT
1 AAATCACTTATAAGATTTGAGCCACTATTTCAAATAATCTTCACATTGACTCAAATTTCATAATT
* ** * ** *
1037513 TATCAATATTTATGTTAGATATGCTTGACTCTACTTACAATGTAAGTCTCATAATCTTCTCCTAT
66 TATCAATATTCATACTAGACATAATTGACTCCACTTACAATGTAAGTCTCATAATCTTCTCCTAT
* * * * * * *
1037578 GACGAAATTGGTAGATGCTGCAAACTTAATTGGATTTGATTGAGTATGGTATGGAAACCTATTAA
131 GACAAAATTAGTAAACGCTACAAACTTAATT-GA-TGGATTGAGTATGGTATGAAAACCTATTAA
1037643 GTGATAAAT
194 GTGATAAAT
* *
1037652 AAATCACTTATAAGATTTGAGCCACTATTTCAAATAATCTTTATATTGACTCAAATTTCATAATT
1 AAATCACTTATAAGATTTGAGCCACTATTTCAAATAATCTTCACATTGACTCAAATTTCATAATT
* * *
1037717 TATCAATCTTCATACTAGACATAATTGGCTCCACTTACAATGTAAGTCTCATAATCTTCTCTTAT
66 TATCAATATTCATACTAGACATAATTGACTCCACTTACAATGTAAGTCTCATAATCTTCTCCTAT
** * * *
1037782 GGTAAAATTAGTAAACGCTACAAACTTAATTGATGGATTGAGTTTGGTATGAAAATCTGTTAAGT
131 GACAAAATTAGTAAACGCTACAAACTTAATTGATGGATTGAGTATGGTATGAAAACCTATTAAGT
1037847 GATAA
196 GATAA
1037852 CTTTCAAATT
Statistics
Matches: 171, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
202 32 0.19
203 2 0.01
204 137 0.80
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (202 bp):
AAATCACTTATAAGATTTGAGCCACTATTTCAAATAATCTTCACATTGACTCAAATTTCATAATT
TATCAATATTCATACTAGACATAATTGACTCCACTTACAATGTAAGTCTCATAATCTTCTCCTAT
GACAAAATTAGTAAACGCTACAAACTTAATTGATGGATTGAGTATGGTATGAAAACCTATTAAGT
GATAAAT
Found at i:1049425 original size:14 final size:14
Alignment explanation
Indices: 1049406--1049433 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1049396 GCATAAAATT
1049406 GTCTAACAGTTTGA
1 GTCTAACAGTTTGA
1049420 GTCTAACAGTTTGA
1 GTCTAACAGTTTGA
1049434 ACAGGGTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
GTCTAACAGTTTGA
Found at i:1065590 original size:53 final size:53
Alignment explanation
Indices: 1065522--1065642 Score: 145
Period size: 53 Copynumber: 2.3 Consensus size: 53
1065512 CATAACAGCT
* * * *
1065522 GTTAAATGAGAAAAAGC-CCATTTACAAGGGTTAACAATCAGAGTAGAATTGG
1 GTTACATGAGAAAAAGCACCATTTACAAGGGTTAACAATCAGAGCAAAACTGG
* * * *
1065574 CGTTACATGAGAAAAAGCACTATTTAGAATGGTTAGCAATCAGAGCAAAACTGG
1 -GTTACATGAGAAAAAGCACCATTTACAAGGGTTAACAATCAGAGCAAAACTGG
*
1065628 TTTACATGAGAAAAA
1 GTTACATGAGAAAAA
1065643 AACCACTGTT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 30 0.52
54 28 0.48
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.23
Consensus pattern (53 bp):
GTTACATGAGAAAAAGCACCATTTACAAGGGTTAACAATCAGAGCAAAACTGG
Found at i:1065669 original size:55 final size:54
Alignment explanation
Indices: 1065522--1065673 Score: 132
Period size: 54 Copynumber: 2.8 Consensus size: 54
1065512 CATAACAGCT
* * * * * * *
1065522 GTTAAATGAGAAAAAGCC-C-ATTTACAAGGGTTAACAATCAGAGTAGAATTGGC
1 GTTACATGAGAAAAA-CCACTATTTAGAATGATTAACAATCAGAGCAAAACTGGC
* * *
1065575 GTTACATGAGAAAAAGCACTATTTAGAATGGTTAGCAATCAGAGCAAAACTGG-
1 GTTACATGAGAAAAACCACTATTTAGAATGATTAACAATCAGAGCAAAACTGGC
* *
1065628 TTTACATGAGAAAAAAACCACTGTTTAGAA-GAATTAACAATCAGAG
1 GTTACATGAG--AAAAACCACTATTTAGAATG-ATTAACAATCAGAG
1065674 TAGATCCTGC
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
52 1 0.01
53 24 0.30
54 28 0.35
55 28 0.35
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.23
Consensus pattern (54 bp):
GTTACATGAGAAAAACCACTATTTAGAATGATTAACAATCAGAGCAAAACTGGC
Found at i:1066690 original size:95 final size:94
Alignment explanation
Indices: 1066563--1066747 Score: 291
Period size: 95 Copynumber: 2.0 Consensus size: 94
1066553 CTAGATTCCA
*
1066563 AGATACATGCTATGCTCTAAAGGATAAAACATAGATTCAGATGAAGT-CATAACTTATATAACAT
1 AGATACATGCTATGCTATAAAGGATAAAACATAGATTCAGATGAAGTCCA-AACTTATATAACAT
* *
1066627 ACATAGTAAAGAACAAAGATAACCTGTCCT
65 ACATAGCAAACAACAAAGATAACCTGTCCT
*
1066657 AGATATATGCTATGCTATCAAAGGATAAAACATAGATTCAGATGAAGTCCAAACTTATATAACAT
1 AGATACATGCTATGCTAT-AAAGGATAAAACATAGATTCAGATGAAGTCCAAACTTATATAACAT
* *
1066722 ATATAGCAAACAACAAATATAACCTG
65 ACATAGCAAACAACAAAGATAACCTG
1066748 ATGAAAAATC
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
94 16 0.19
95 65 0.78
96 2 0.02
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (94 bp):
AGATACATGCTATGCTATAAAGGATAAAACATAGATTCAGATGAAGTCCAAACTTATATAACATA
CATAGCAAACAACAAAGATAACCTGTCCT
Found at i:1067889 original size:15 final size:16
Alignment explanation
Indices: 1067864--1067893 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1067854 TTCAAACGAA
1067864 AATAGAAAAGAAAAAG
1 AATAGAAAAGAAAAAG
1067880 AATA-AAAAGAAAAA
1 AATAGAAAAGAAAAA
1067894 TGACCTACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (16 bp):
AATAGAAAAGAAAAAG
Found at i:1069793 original size:20 final size:20
Alignment explanation
Indices: 1069768--1069808 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1069758 TCTTCTTTGA
*
1069768 ATATAGAAAGGAACTGGTTT
1 ATATAGAAAGAAACTGGTTT
1069788 ATATAGAAAGAAACTGGTTT
1 ATATAGAAAGAAACTGGTTT
1069808 A
1 A
1069809 GTGTCCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (20 bp):
ATATAGAAAGAAACTGGTTT
Found at i:1072570 original size:15 final size:16
Alignment explanation
Indices: 1072550--1072579 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1072540 TAGGTCTTTT
1072550 TTTTTCTTTT-TATTC
1 TTTTTCTTTTCTATTC
1072565 TTTTTCTTTTCTATT
1 TTTTTCTTTTCTATT
1072580 TTCGTTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTCTTTTCTATTC
Found at i:1085745 original size:20 final size:20
Alignment explanation
Indices: 1085708--1085746 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1085698 GAAAATTTTA
*
1085708 TTTTATAAAAAATTTTAAAT
1 TTTTATAAAAAATATTAAAT
* *
1085728 TTTTATTAAATATATTAAA
1 TTTTATAAAAAATATTAAA
1085747 ATTAAATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTATAAAAAATATTAAAT
Found at i:1091999 original size:37 final size:37
Alignment explanation
Indices: 1091945--1092023 Score: 124
Period size: 37 Copynumber: 2.2 Consensus size: 37
1091935 ACATATCACT
**
1091945 TATG-GGAATATTATAAGAGCTAAAAAAAGAATTAGA
1 TATGTGGAATATTATAAGAGAAAAAAAAAGAATTAGA
*
1091981 TATGTGGAATATTATAAGAGAAAAAAAAATAATTAGA
1 TATGTGGAATATTATAAGAGAAAAAAAAAGAATTAGA
1092018 TATGTG
1 TATGTG
1092024 ATAGGTAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 4 0.10
37 35 0.90
ACGTcount: A:0.52, C:0.01, G:0.19, T:0.28
Consensus pattern (37 bp):
TATGTGGAATATTATAAGAGAAAAAAAAAGAATTAGA
Found at i:1097007 original size:41 final size:41
Alignment explanation
Indices: 1096945--1097027 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
1096935 GAACATTCAT
1096945 ATCAGTTAATTATGAGCAATTTAAATATAATATTATTGTCA
1 ATCAGTTAATTATGAGCAATTTAAATATAATATTATTGTCA
*
1096986 ATCAGTTAATTATGAGTAATTTAAATATAATATTATTGTCA
1 ATCAGTTAATTATGAGCAATTTAAATATAATATTATTGTCA
1097027 A
1 A
1097028 CAATGGTATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (41 bp):
ATCAGTTAATTATGAGCAATTTAAATATAATATTATTGTCA
Found at i:1103811 original size:2 final size:2
Alignment explanation
Indices: 1103806--1103838 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1103796 TTTTTTTTGT
*
1103806 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1103839 GTAAGTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1104602 original size:32 final size:32
Alignment explanation
Indices: 1104561--1104625 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1104551 TTTTTGCAGT
1104561 TTCTCTGCTTTGGATTATTAAGAAAGTAAAAA
1 TTCTCTGCTTTGGATTATTAAGAAAGTAAAAA
1104593 TTCTCTGCTTTGGATTATTAAGAAAGTAAAAA
1 TTCTCTGCTTTGGATTATTAAGAAAGTAAAAA
1104625 T
1 T
1104626 ATTATTCCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (32 bp):
TTCTCTGCTTTGGATTATTAAGAAAGTAAAAA
Found at i:1105457 original size:28 final size:28
Alignment explanation
Indices: 1105409--1105462 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1105399 ATCTTTTTAT
* * *
1105409 AAAATTTAATCTGAATCTAAATTATTCA
1 AAAATTTAATATGAATATAAAATATTCA
*
1105437 AAAATTTAATATGACTATAAAATATT
1 AAAATTTAATATGAATATAAAATATT
1105463 GAGAGTCTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (28 bp):
AAAATTTAATATGAATATAAAATATTCA
Found at i:1121394 original size:29 final size:29
Alignment explanation
Indices: 1121362--1121437 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 29
1121352 GAACTTTAAT
* * *
1121362 AAAATATTTAATGTAATATTTAAATTTTA
1 AAAATATTTAATATAATATATAAATTATA
* *
1121391 AAAATCTTTAATATAGTATATAAATTATA
1 AAAATATTTAATATAATATATAAATTATA
**
1121420 AATTTA-TTAAT-TAATATA
1 AAAATATTTAATATAATATA
1121438 ATATTTAAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 6 0.16
28 5 0.13
29 27 0.71
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (29 bp):
AAAATATTTAATATAATATATAAATTATA
Found at i:1121542 original size:28 final size:29
Alignment explanation
Indices: 1121511--1121597 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 29
1121501 TATGATATTA
*
1121511 ATTAATAAA-TTCATAATTCAAATATCAC
1 ATTAAAAAATTTCATAATTCAAATATCAC
* * **
1121539 ATTAAAAAATTTTATAATTTAAATATCTT
1 ATTAAAAAATTTCATAATTCAAATATCAC
* * *
1121568 ATTAAATATTTTACTATAATTCAAAAATCA
1 ATTAAAAAATTT-C-ATAATTCAAATATCA
1121598 GTAGCCCGAA
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
28 8 0.18
29 25 0.56
31 12 0.27
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.41
Consensus pattern (29 bp):
ATTAAAAAATTTCATAATTCAAATATCAC
Found at i:1132946 original size:2 final size:2
Alignment explanation
Indices: 1132939--1132971 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1132929 TACACCACAA
1132939 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1132972 TCATTACAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1152303 original size:2 final size:2
Alignment explanation
Indices: 1152298--1152324 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1152288 TGGACCAGAA
1152298 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1152325 TTCTTCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1155997 original size:6 final size:6
Alignment explanation
Indices: 1155988--1156034 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
1155978 GATGGCCCCA
* * *
1155988 ATGGGG ATGGGA ATGGGG ATGCGG ATGGGG ATGGGG ATGGGC ATGGG
1 ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG ATGGGG ATGGG
1156035 TTTCATGGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.19, C:0.04, G:0.60, T:0.17
Consensus pattern (6 bp):
ATGGGG
Found at i:1158182 original size:2 final size:2
Alignment explanation
Indices: 1158175--1158206 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1158165 AATGTTCATT
1158175 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1158207 ATTATTAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1166308 original size:10 final size:10
Alignment explanation
Indices: 1166276--1166309 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1166266 CATGGTGGAG
1166276 TATGTTTATA
1 TATGTTTATA
1166286 TAGTGTTTATA
1 TA-TGTTTATA
*
1166297 TATGTATATA
1 TATGTTTATA
1166307 TAT
1 TAT
1166310 CTTGTTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (10 bp):
TATGTTTATA
Found at i:1169620 original size:2 final size:2
Alignment explanation
Indices: 1169613--1169637 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1169603 CGGAGGGAAC
1169613 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1169638 ATAAGTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1172148 original size:3 final size:3
Alignment explanation
Indices: 1172142--1172205 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
1172132 AAAAGGGTTT
1172142 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1172190 TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA T
1172206 AATAATAATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:1172210 original size:3 final size:3
Alignment explanation
Indices: 1172204--1172244 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1172194 GATGATGATG
1172204 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1172245 GTGTAAGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1178030 original size:23 final size:24
Alignment explanation
Indices: 1178000--1178047 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
1177990 GTAATTCGCC
1178000 AATAATTTCAACAAT-A-TTATCAA
1 AATAATTTCAA-AATGACTTATCAA
*
1178023 AATAATTTGAAAATGACTTATCAA
1 AATAATTTCAAAATGACTTATCAA
1178047 A
1 A
1178048 TAAAAATTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 11 0.50
24 8 0.36
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AATAATTTCAAAATGACTTATCAA
Found at i:1179149 original size:31 final size:31
Alignment explanation
Indices: 1179108--1179166 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1179098 AAAAAATTTA
1179108 TTCACTAATAAAATAATATCATTTAATTCAT
1 TTCACTAATAAAATAATATCATTTAATTCAT
* *
1179139 TTCATTAATAAAATAATATTATTTAATT
1 TTCACTAATAAAATAATATCATTTAATT
1179167 TATTAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (31 bp):
TTCACTAATAAAATAATATCATTTAATTCAT
Found at i:1183384 original size:2 final size:2
Alignment explanation
Indices: 1183379--1183405 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1183369 TCATATTATC
1183379 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1183406 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1183410 original size:2 final size:2
Alignment explanation
Indices: 1183405--1183453 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1183395 ATATATATAT
1183405 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1183447 AG AG AG A
1 AG AG AG A
1183454 CTAAGAGGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1189111 original size:30 final size:29
Alignment explanation
Indices: 1189038--1189112 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
1189028 AATTTTTTTA
**
1189038 ATTAATTAAACGTTTAAACATTTATATTC
1 ATTAATTAAATTTTTAAACATTTATATTC
* * * *
1189067 ATTTATTTAATTTTTAAATATTTATTTTC
1 ATTAATTAAATTTTTAAACATTTATATTC
1189096 ATATAATTAAATTTTTA
1 AT-TAATTAAATTTTTA
1189113 TTAGACAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 25 0.68
30 12 0.32
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (29 bp):
ATTAATTAAATTTTTAAACATTTATATTC
Found at i:1192488 original size:57 final size:57
Alignment explanation
Indices: 1192425--1192538 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
1192415 AAATTTTTTG
* *
1192425 TTTTTTGTTGTTTGATGATAGATCTGGAAAGAATAGGACTTCATTGTTTAAGATCTA
1 TTTTTTGTTGTTTAATGATAAATCTGGAAAGAATAGGACTTCATTGTTTAAGATCTA
1192482 TTTTTTGTTGTTTAATGATAAATCTGGAAAGAATAGGACTTCATTGTTTAAGATCTA
1 TTTTTTGTTGTTTAATGATAAATCTGGAAAGAATAGGACTTCATTGTTTAAGATCTA
1192539 GTGTGCAGTG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (57 bp):
TTTTTTGTTGTTTAATGATAAATCTGGAAAGAATAGGACTTCATTGTTTAAGATCTA
Found at i:1192960 original size:100 final size:100
Alignment explanation
Indices: 1192857--1193054 Score: 339
Period size: 100 Copynumber: 2.0 Consensus size: 100
1192847 ACAATTGGAT
1192857 TTTTTTCTTCTTGTGCTG-TTTGTTTTT-TT-ATATTGTTCACAATTTACTGCCCCCTGAGTTTT
1 TTTTTTCTTCTTGTGCTGTTTTGTTTTTCTTAATATTGTTCACAATTTACTG-CCCC-GAGTTTT
*
1192919 AAGCTTGTCATCTGTGTGATTACTTATATATAAGATA
64 AAGCTTGTCATCTGTCTGATTACTTATATATAAGATA
*
1192956 TTTTTTCTTCTTGTGCTGTTTTTTTTTTCTTAATATTGTTCACAATTTACTGCCCCGAGTTTTAA
1 TTTTTTCTTCTTGTGCTGTTTTGTTTTTCTTAATATTGTTCACAATTTACTGCCCCGAGTTTTAA
1193021 GCTTGTCATCTGTCTGATTACTTATATATAAGAT
66 GCTTGTCATCTGTCTGATTACTTATATATAAGAT
1193055 CAATTCATCT
Statistics
Matches: 94, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
99 18 0.19
100 50 0.53
101 6 0.06
102 20 0.21
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (100 bp):
TTTTTTCTTCTTGTGCTGTTTTGTTTTTCTTAATATTGTTCACAATTTACTGCCCCGAGTTTTAA
GCTTGTCATCTGTCTGATTACTTATATATAAGATA
Found at i:1203948 original size:5 final size:5
Alignment explanation
Indices: 1203931--1203983 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
1203921 TAAACTGATA
*
1203931 AAATT AAATTT AAATT AAA-T AAATTT AAA-- AAATT AAACT AAATT AAATT
1 AAATT AAA-TT AAATT AAATT AAA-TT AAATT AAATT AAATT AAATT AAATT
1203980 AAAT
1 AAAT
1203984 ATTAAATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
3 3 0.07
4 4 0.10
5 25 0.61
6 9 0.22
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:1203953 original size:29 final size:28
Alignment explanation
Indices: 1203921--1203978 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
1203911 TTAATCAAAT
* *
1203921 TAAACTGATAAAATTAAATTTAAATTAAA
1 TAAACTGAAAAAATTAAA-CTAAATTAAA
* *
1203950 TAAATTTAAAAAATTAAACTAAATTAAA
1 TAAACTGAAAAAATTAAACTAAATTAAA
1203978 T
1 T
1203979 TAAATATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (28 bp):
TAAACTGAAAAAATTAAACTAAATTAAA
Found at i:1203973 original size:28 final size:31
Alignment explanation
Indices: 1203930--1203989 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
1203920 TTAAACTGAT
*
1203930 AAAATTAAATTTAAATTAAA-TAAAT-TTAA
1 AAAATTAAATCTAAATTAAATTAAATATTAA
1203959 AAAATTAAA-CTAAATTAAATTAAATATTAA
1 AAAATTAAATCTAAATTAAATTAAATATTAA
1203989 A
1 A
1203990 TATTTATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 9 0.32
29 14 0.50
30 5 0.18
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (31 bp):
AAAATTAAATCTAAATTAAATTAAATATTAA
Found at i:1205966 original size:2 final size:2
Alignment explanation
Indices: 1205959--1205991 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1205949 TGATGTAACT
1205959 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1205992 TATTGGTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1213812 original size:8 final size:8
Alignment explanation
Indices: 1213796--1213828 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
1213786 TTTAACATAC
*
1213796 ACATTTAT
1 ACATATAT
1213804 ACATATAT
1 ACATATAT
1213812 ACATATAT
1 ACATATAT
1213820 ACATATAT
1 ACATATAT
1213828 A
1 A
1213829 TAGTCTTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (8 bp):
ACATATAT
Found at i:1216246 original size:2 final size:2
Alignment explanation
Indices: 1216234--1216306 Score: 130
Period size: 2 Copynumber: 37.0 Consensus size: 2
1216224 CTAATTCCTG
*
1216234 CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1216276 CT CT CT CT CT CT -T CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1216307 TCAACCCCTG
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:1226404 original size:16 final size:15
Alignment explanation
Indices: 1226385--1226426 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
1226375 AAAATATAAC
1226385 ATTTAATAATTTTAAA
1 ATTT-ATAATTTTAAA
*
1226401 ATTTA-AATTTTAAC
1 ATTTATAATTTTAAA
*
1226415 ACTTATAATTTT
1 ATTTATAATTTT
1226427 TTTATTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 12 0.52
15 7 0.30
16 4 0.17
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTATAATTTTAAA
Found at i:1226644 original size:3 final size:3
Alignment explanation
Indices: 1226636--1226662 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1226626 TATAGCATTT
1226636 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1226663 CCCGTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1227783 original size:16 final size:15
Alignment explanation
Indices: 1227757--1227796 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
1227747 TTAAAATATT
1227757 ATAAAATAATATAAG
1 ATAAAATAATATAAG
*
1227772 ATAAATATAATATAAA
1 ATAAA-ATAATATAAG
1227788 ATTAAAATA
1 A-TAAAATA
1227797 TAAAATAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 13 0.59
17 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
ATAAAATAATATAAG
Found at i:1227797 original size:18 final size:16
Alignment explanation
Indices: 1227757--1227804 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
1227747 TTAAAATATT
*
1227757 ATAAA-ATAATATAAG
1 ATAAATATAATATAAA
1227772 ATAAATATAATATAAA
1 ATAAATATAATATAAA
*
1227788 ATTAAAATATAAAATAA
1 A-T-AAATATAATATAA
1227805 CACTATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 1 0.04
18 12 0.43
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (16 bp):
ATAAATATAATATAAA
Found at i:1227903 original size:31 final size:33
Alignment explanation
Indices: 1227868--1227964 Score: 87
Period size: 32 Copynumber: 3.1 Consensus size: 33
1227858 ATATTTTATG
*
1227868 TTTTTATATTTAAAT-GAAT-TATAATATA-AAA
1 TTTTTATATTTAAATATAATATA-AATATATAAA
*
1227899 TTTTTATA-TAAAATATAATATAAATATATAAA
1 TTTTTATATTTAAATATAATATAAATATATAAA
* * * * *
1227931 TTTTAATATTT-TATATTATATCAATATACAAA
1 TTTTTATATTTAAATATAATATAAATATATAAA
1227963 TT
1 TT
1227965 ATAGATCTAC
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
30 5 0.09
31 17 0.31
32 31 0.57
33 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (33 bp):
TTTTTATATTTAAATATAATATAAATATATAAA
Found at i:1229747 original size:43 final size:43
Alignment explanation
Indices: 1229685--1229766 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
1229675 ATTTTGATTT
1229685 GAACTAAGCATGCCCTTGTCGACCAAATAATTCAATTGGCTAC
1 GAACTAAGCATGCCCTTGTCGACCAAATAATTCAATTGGCTAC
* *
1229728 GAACTAAGCATGCCTTTGTCGACCGAATAATTCAATTGG
1 GAACTAAGCATGCCCTTGTCGACCAAATAATTCAATTGG
1229767 TTAAGTTACT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (43 bp):
GAACTAAGCATGCCCTTGTCGACCAAATAATTCAATTGGCTAC
Found at i:1235477 original size:7 final size:7
Alignment explanation
Indices: 1235457--1235513 Score: 53
Period size: 7 Copynumber: 7.7 Consensus size: 7
1235447 TTATTTTATT
1235457 TTATTTA
1 TTATTTA
1235464 TTA-TTA
1 TTATTTA
1235470 TTATTTA
1 TTATTTA
1235477 TTAATATATA
1 TT-AT-T-TA
*
1235487 TTTTTTA
1 TTATTTA
1235494 TTATTTA
1 TTATTTA
*
1235501 TTTATTAA
1 -TTATTTA
1235509 TTATT
1 TTATT
1235514 AATATGCATT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
6 6 0.14
7 21 0.50
8 9 0.21
9 2 0.05
10 4 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TTATTTA
Found at i:1235513 original size:35 final size:36
Alignment explanation
Indices: 1235448--1235533 Score: 113
Period size: 35 Copynumber: 2.4 Consensus size: 36
1235438 TTTGTATTTT
*
1235448 TATTTTATTTTATTTATTATTATTATTTATTAATATA
1 TATTTT-TTTTATTTATTATTATTAATTATTAATATA
*
1235485 TATTTTTTATTATTTA-T-TTATTAATTATTAATATG
1 TATTTTTT-TTATTTATTATTATTAATTATTAATATA
*
1235520 CATTTTTTTTATTT
1 TATTTTTTTTATTT
1235534 TATATTGATT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
34 6 0.13
35 23 0.51
36 3 0.07
37 13 0.29
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (36 bp):
TATTTTTTTTATTTATTATTATTAATTATTAATATA
Found at i:1236342 original size:58 final size:58
Alignment explanation
Indices: 1236280--1236615 Score: 434
Period size: 58 Copynumber: 5.8 Consensus size: 58
1236270 TTTTTAATGA
* *
1236280 TTTTCTT-AAAATAAAATTCTAAAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAAT
1 TTTTCTTGAAAATAAAATT-TTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
* * *
1236338 TTTTCTTGAAAAT-AAGTTTTCTAAAAAATATTTTCGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAAATAAAATTTT-AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
* * * *
1236396 TTTTCTTGAAAAT-AATTTTTTAAAAAATATTTTTGAGGAAAAGGTAAAAGTATCAAT
1 TTTTCTTGAAAATAAAATTTTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
*
1236453 TTTTCTT-AAAAGTAAAATTTTTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAAA-TAAAATTTTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
* *
1236511 TTTTCTTAAAAATAAATGTTTTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAAATAAA-ATTTTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
* * *
1236570 TTTT-TTCAAAATTAAAGTTTTAGAAAAATA-TTTTG-GGAAAAAGTTG
1 TTTTCTTGAAAA-TAAAATTTTAAAAAAATATTTTTGAGG-AAAAGTTG
1236616 GAAGCACCTA
Statistics
Matches: 254, Mismatches: 16, Indels: 17
0.89 0.06 0.06
Matches are distributed among these distances:
56 6 0.02
57 56 0.22
58 135 0.53
59 57 0.22
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (58 bp):
TTTTCTTGAAAATAAAATTTTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
Found at i:1236434 original size:115 final size:116
Alignment explanation
Indices: 1236280--1236656 Score: 468
Period size: 115 Copynumber: 3.2 Consensus size: 116
1236270 TTTTTAATGA
* *
1236280 TTTTCTT-AAAATAAAAT-TCTAAAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTC
1 TTTTCTTAAAAAT-AAATGTTTTAAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTC
1236343 TTGAAAA-T-AAGTTTTCTAAAAAATATTTTCGAGGAAAAGTTGAAAGTATCAAT
65 TT-AAAAGTAAAGTTTT-TAAAAAATATTTT-GAGGAAAAGTTGAAAGTATCAAT
* * *
1236396 TTTTCTTGAAAAT-AAT-TTTTTAAAAAATATTTTTGAGGAAAAGGTAAAAGTATCAATTTTTCT
1 TTTTCTTAAAAATAAATGTTTTAAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCT
*
1236459 TAAAAGTAAAATTTTTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
66 TAAAAGTAAAGTTTTTAAAAAATA-TTTTGAGGAAAAGTTGAAAGTATCAAT
*
1236511 TTTTCTTAAAAATAAATGTTTTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTT-T
1 TTTTCTTAAAAATAAATGTTTTAAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCT
* * * * *
1236575 TCAAAATTAAAG-TTTTAGAAAAATATTTTG-GGAAAAAGTTGGAAGCACCTAT
66 T-AAAAGTAAAGTTTTTA-AAAAATATTTTGAGG-AAAAGTTGAAAGTATCAAT
* *
1236627 TTTCCTTAACAAA-AAACGTTTTAAAGAAAA
1 TTTTCTTAA-AAATAAATGTTTTAAA-AAAA
1236657 GTTGAAAGTA
Statistics
Matches: 233, Mismatches: 17, Indels: 21
0.86 0.06 0.08
Matches are distributed among these distances:
114 4 0.02
115 94 0.40
116 66 0.28
117 69 0.30
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.38
Consensus pattern (116 bp):
TTTTCTTAAAAATAAATGTTTTAAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCT
TAAAAGTAAAGTTTTTAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAAT
Found at i:1236648 original size:58 final size:57
Alignment explanation
Indices: 1236302--1236651 Score: 340
Period size: 58 Copynumber: 6.1 Consensus size: 57
1236292 AAAATTCTAA
* * *
1236302 AAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTT--GAAAATAAGTTTTCT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCTTAACAAAAAAAG-TTT-T
* * * **
1236360 AAAAAATATTTTCGAGGAAAAGTTGAAAGTATCAATTTTTCTTGA-AAATAATTTTTT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCTTAACAAAAAAAGTTTT
* * * *
1236417 AAAAAATATTTTTGAGGAAAAGGTAAAAGTATCAATTTTTCTTAA-AAGTAAAATTTTT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCTTAACAA-AAAAAGTTTT
*
1236475 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAA-AAATAAATGTTTT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCTTAACAAA-AAAAGTTTT
*
1236533 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT-TT-TCAAAATTAAAGTTTT
1 -AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTAACAAAA--AAAGTTTT
* * * * *
1236591 AGAAAAATA-TTTTG-GGAAAAAGTTGGAAGCACCTATTTTCCTTAACAAAAAACGTTTT
1 A-AAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTT-CTTAACAAAAAAAGTTTT
1236649 AAA
1 AAA
1236652 GAAAAGTTGA
Statistics
Matches: 253, Mismatches: 26, Indels: 27
0.83 0.08 0.09
Matches are distributed among these distances:
56 3 0.01
57 75 0.30
58 129 0.51
59 41 0.16
60 5 0.02
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (57 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTAACAAAAAAAGTTTT
Found at i:1237392 original size:23 final size:23
Alignment explanation
Indices: 1237349--1237392 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
1237339 TTTTGTATAA
*
1237349 ATTTTTTTTATTCATTCATGTTT
1 ATTTTTTTTATTAATTCATGTTT
*
1237372 ATTTATTTTTGTTAATT-ATGT
1 ATTT-TTTTTATTAATTCATGT
1237393 CATTCATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (23 bp):
ATTTTTTTTATTAATTCATGTTT
Found at i:1237965 original size:23 final size:23
Alignment explanation
Indices: 1237938--1237985 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1237928 TTAGCTCCTT
1237938 GTGAGTCATCCAACGAAGTAAGG
1 GTGAGTCATCCAACGAAGTAAGG
1237961 GTGAGTCATCCAACGAAGTAAGG
1 GTGAGTCATCCAACGAAGTAAGG
1237984 GT
1 GT
1237986 CCAGTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (23 bp):
GTGAGTCATCCAACGAAGTAAGG
Found at i:1247213 original size:19 final size:19
Alignment explanation
Indices: 1247189--1247232 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
1247179 TATTATGCTT
*
1247189 AAAAAAATAAAAAATAAAATG
1 AAAAAAA-ATAAAA-AAAATG
1247210 AAAAAAAATAAAAAAAATG
1 AAAAAAAATAAAAAAAATG
1247229 AAAA
1 AAAA
1247233 TGAAGAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 5 0.23
21 7 0.32
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (19 bp):
AAAAAAAATAAAAAAAATG
Found at i:1247217 original size:25 final size:25
Alignment explanation
Indices: 1247189--1247236 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
1247179 TATTATGCTT
*
1247189 AAAAAAATAAAAAAT-AAAATGAAA
1 AAAAAAAAAAAAAATGAAAATGAAA
*
1247213 AAAAATAAAAAAAATGAAAATGAA
1 AAAAAAAAAAAAAATGAAAATGAA
1247237 GAGAAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (25 bp):
AAAAAAAAAAAAAATGAAAATGAAA
Done.